Patrick Fuller
a8ff003d8c
IPython 3D view now has a draggable resizer
2014-09-10 11:37:36 -05:00
Patrick Fuller
7fa5c42e31
Updated IPython rendering to use v2.0 style, now works on nbviewer and on local machines
2014-08-24 12:54:59 -05:00
Geoff Hutchison
5f083787cf
Fix pybel test failure by renaming expected output to UNL from LIG
2014-03-15 15:59:37 -04:00
Matt Swain
668e5f8179
Bump python bindings version to 1.8.1
2014-01-28 17:02:31 +00:00
Matt Swain
9962917d9d
Add more info to python README and revert package name change
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Change the python bindings package name back to 'openbabel', but make clear in the Python README that this is just the python bindings, not the main Open Babel library, just in case anyone stumbles across the PyPI page by accident.
2014-01-28 10:48:59 +00:00
Matt Swain
099f67badb
Change python bindings package name to openbabel-python
2014-01-24 11:11:52 +00:00
Matt Swain
e65bf4bfbc
Make pkg-config check more robust and allow manual override
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Add a sensible fallback if pkg-config fails to locate the Open Babel include and library directories, and a helpful error message if that fallback also fails.
Allow Open Babel include and library directories to be manually specified as command line options to setup.py using the build_ext command with -I and -L options.
2014-01-20 18:22:13 +00:00
Matt Swain
d6a44bcd40
Ensure build_ext runs before build_py
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The setup.py build and install commands run a number of subcommands, including build_ext, which runs SWIG to generate openbabel.py, and build_py, which copies openbabel.py and other python sources to the build directory.
The default ordering is for build_py to be run before build_ext, causing errors as build_py attempts to copy openbabel.py before it exists. This change ensures build_ext is always run first at the start of both the build and install commands.
2014-01-20 18:07:07 +00:00
Matt Swain
b94f4b7f83
Add proper python README
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- Convert README to restructuredtext format so it displays correctly on PyPI
- Update email address to current mailing list
- Tidy up setup.py
2014-01-20 17:58:42 +00:00
Patrick Fuller
668536d591
Improved error messages of calccharges
2014-01-15 10:52:34 -06:00
Patrick Fuller
1612e84ef9
Small fix
2014-01-15 10:16:39 -06:00
Patrick Fuller
e5ef11f521
Improvements to proposed pybel charge method
2014-01-15 10:05:46 -06:00
Patrick Fuller
843ecae262
Added a charge function
2014-01-14 13:04:55 -05:00
S. Joshua Swamidass
42335bd889
missed setup.py in last committ
2014-01-05 08:57:27 -10:00
S. Joshua Swamidass
3cf839f34e
Rewrote setup.py so that it can independentley install python bindings. Symbolic links to swig files added to enable this.
2014-01-05 08:51:47 -10:00
Patrick Fuller
e0b2dc2c67
Changed url of 3d molecule viewer
2013-12-24 13:03:37 -05:00
Patrick Fuller
d869efe9ac
Reduced footprint of 3D ipython rendering
2013-12-23 16:24:52 -05:00
Patrick Fuller
d02d57f3f9
2D/3D toggle now accessible by pybel.ipython_3d boolean
2013-12-09 09:38:12 -06:00
Patrick Fuller
995326303f
pybel.py made PEP8 compliant
2013-12-08 20:49:10 -06:00
Patrick Fuller
d4826d10c3
Rough implementation of Javascript IPython rendering
2013-09-29 17:48:43 -05:00
Maciek Wójcikowski
9c5bad432e
Fix documentation of residues in pybel
2013-03-20 13:33:34 +01:00
Geoff Hutchison
e4804d9c26
Merge pull request #1 from mwojcikowski/master
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Fix missing LPMD file in src/format
2013-03-15 11:10:28 -07:00
Maciek Wójcikowski
7c8a9b6327
Pybel residue support
2013-03-06 13:26:38 +01:00
Björn Grüning
006a9351ad
add ConvertDativeBonds to pybel
2013-03-05 23:37:00 +01:00
Noel O'Boyle
df59c4a630
Drat! Trival fix to re-enable Molecule.draw() after recent changes to PNG2.
2012-10-29 15:26:47 +00:00
Reinis Danne
7366f780bb
setup.py: There are no separate pybel_pyX.py files anymore
2012-10-15 12:18:03 +00:00
Noel O'Boyle
c19f75c45f
scripts/python/testpybel.py: Minor fix to enable failing test to pass. Failures due to the new MOL Chiral Flag data that I stored a while ago.
2012-10-01 20:40:36 +00:00
Geoffrey Hutchison
c08b71defc
Add test Python script from Andrew Dalke.
2012-07-26 19:12:40 +00:00
Noel O'Boyle
2c9aa50fef
pybel.py: Fix for previous commit to remove tabs.
2012-06-26 13:49:31 +00:00
Noel O'Boyle
0e6c1f59ee
Simplify installation of Python bindings: Now there is only one version of pybel.py for Py 2.x and Py 3.x. It also includes support for Jython and IronPython.
2012-06-26 13:43:25 +00:00
Noel O'Boyle
2b13e591d6
testpybel.py: Update for corrected unit cell parameters. I should have checked this in a long time ago...
2012-05-17 12:58:21 +00:00
Noel O'Boyle
00b9359103
Update draw method pybel to remove explicit Hs before calling gen2d.
2011-06-27 08:36:52 +00:00
Noel O'Boyle
57fa747db2
pybel.py: Update pybel versions to draw using the PNG2 format.
2011-06-05 18:40:28 +00:00
Noel O'Boyle
aa2e4eace3
Pybel Python files: Updates on the drawing code using Chris's "P" option for SVG.
2011-05-26 19:34:09 +00:00
Noel O'Boyle
fa4c9d71f0
Update the draw method of Pybel so that it uses our own depiction and 2D layout. I've removed the dependency on OASA (but added optional dependencies on cairo and pyrsvg). Once we have direct depiction on PNG I'll be able to drop the pyrsvg one.
2011-05-16 20:14:36 +00:00
Noel O'Boyle
8972f41fe6
openbabel-csharp.i: Fix Downcast method (was already fixed in 2.2.x but was not merged to trunk)
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pybel.py: Updated to synch with Cinfony.
2011-04-15 07:57:42 +00:00
Geoffrey Hutchison
0ffd9199f1
Patches from Fedora packaging.
2010-12-15 21:45:57 +00:00
Noel O'Boyle
7a83696add
Update docs and Python binding version.
2010-10-26 11:37:36 +00:00
Geoffrey Hutchison
3e71f5a35b
Update website to openbabel.org (long overdue).
2010-10-10 01:24:39 +00:00
Noel O'Boyle
e4f82feb86
testpybel.py: Fix typo in commit of a few days ago. Test should pass now.
2010-10-07 19:03:48 +00:00
Noel O'Boyle
5e87842233
Rename pybel versions for Py 2 and 3 so that they can be imported directly during testing. Associated changes in testpybel setup.py and testbindings.py.
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This fixes a problem running testbindings.py in the testsuite on Windows. (It was importing the globalling installed pybel.py)
2010-10-04 12:37:06 +00:00
Noel O'Boyle
7fa8ad6093
* scripts/python/examples/testpybel.py: Make test of number of descriptors more general. Should pass now.
2010-10-02 19:23:48 +00:00
Noel O'Boyle
0c0095ba53
* scripts/python/pybel_py*.x.py: Synch with cinfony. Add support for
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MCDL 2D coordinate generation when calling 'draw()'. MCDL is the
default. To use OASA, specify method="oasa"
2010-09-09 21:42:22 +00:00
Noel O'Boyle
7cf0b904e4
Get pybel tests to pass once again on Windows.
2010-08-11 15:45:33 +00:00
Noel O'Boyle
acd2e935e2
* Set svn:eol-style to native for all text files.
2010-06-03 14:29:31 +00:00
Noel O'Boyle
d102bde7ad
Minor fix for installing Python bindings on Linux
2010-06-01 08:36:30 +00:00
Noel O'Boyle
56b776be94
More corrections due to new location of swig outputs
2010-05-09 19:45:42 +00:00
Noel O'Boyle
f57656970e
2010-04-26 Noel O'Boyle
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* test/CMakeLists.txt, test/testbindings.py, test/test_pybel.py:
Separate the pybel tests from the Python binding tests
* scripts/python/examples/testpybel.py: Get the Pybel tests to pass on
Linux
* scripts/CMakeLists.txt: Force the Python build to output to
scripts/pybuild. Otherwise it created a temporary folder whose name
differed from platform to platform (e.g. lib.linux-x86_64.2.6) which
made it difficult to handle automatically.
2010-04-27 09:35:35 +00:00
Noel O'Boyle
3d6dc5d93b
2010-04-25 Noel O'Boyle
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* test\CMakeLists.txt, test\testbindings.py, test\testexample.py:
Enable the use of the Python bindings for testing. Run the Pybel
tests. Add a simple example test as a template.
* scripts\python\examples\testpybel.py: Get the Pybel tests to pass
2010-04-25 11:30:10 +00:00
Noel O'Boyle
5934edee4b
2010-03-13 Noel O'Boyle
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* scripts/CMakeLists.txt, scripts/python/setup.py: Compile the
SWIG bindings manually.
2010-03-13 11:57:35 +00:00
